Infrastructure for learning and representing protein motions from structural data
Joined August 2025
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Open data. Public logbooks. No waiting for publications. The DiffUSE Project is redesigning the structural biology pipeline from sample prep to modeling, all in the open. Meet DiffUSE: youtu.be/_DILlMou1GM?si=AwWI…
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The DiffUSE Project retweeted
To realize AI for science, we have to change how we feed the machine. sampleworks, the first publication from @radialscience‘s @diffuseproject is a step: an open, modular platform for building and benchmarking structure predictors against experimental data 👇
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(1 / 3) First scholarly publication from The DiffUSE Project. sampleworks: an open, modular platform for generating and evaluating biomolecular conformational ensembles from structure predictors guided by experimental data. doi.org/10.82153/jkxj-tw08
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(2 / 3) sampleworks was built openly and is made to be easily built upon for many different methods development approaches. github.com/diff-use/samplewo…
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We tested how well current models recover alternative conformations from the PDB. Success varied widely across proteins, a sign that models rely on memorization rather than true generalization, pointing to new training paradigms for structure-ensemble prediction.
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Want to shape the future of structural biology? We are seeking a Project Manager to help lead the DiffUSE Project, guiding ML researchers, computational scientists, national labs, and university partners. Apply: buff.ly/gZlj9AP #StructuralBiology #MachineLearning #Hiring
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The DiffUSE Project wants examples where structural heterogeneity matters but cannot be encoded in PDBx/mmCIF. X-ray, cryo-EM, time-resolved, multi-map, or fragment screening data welcome. Submit yours: diffuse.science/submit/
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The DiffUSE Project retweeted
May 18
Simulations can be valuable but there is a huge need for scalable experiments that probe protein dynamics- of course we're expanding our work here and there's also great work from others @HWaymentSteele @ginaelnesr @BasileWicky @diffUSEproject
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ICYMI: The latest Tortured Proteins Department episode. @stephanie_mul and @fraser_lab on: NIH strategic plan comments (due 5/26), AI lab guidelines, two new cryo-EM preprints, training scientists for what's next diffuse.science/posts/TTPD-1…
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The DiffUSE Project retweeted
May 4
Love all the AI-native initiatives for research sharing I’m starting to see pop up across the ecosystem. If you’re building in this space, I’d love to hear from you as there may be some synergies or opportunities across our open science efforts at @AsteraInstitute
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The DiffUSE Project retweeted
May 5
This tube is a library of bacteria with every single-base-pair genome mutation, all DNA-barcoded.🧪Growth barcode sequencing = data on millions of mutations.
📄 Report: biorxiv.org/content/10.64898…
Retweet if you want more data, and read on if you want to use the library! 🧵
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🎉🎉🎉
I'm ecstatic to share that I'm joining @diffUSEproject full-time as Scientific Program Director at @AsteraInstitute.
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Hosted in partnership with the DiffUSE Project! 🎉👇
Year 3 of Conformational Ensembles Conference! The most compelling questions in structural biology cannot be effectively addressed with a single structure. We have a stellar lineup of people looking at and answering these questions. More information: conformationalensembles.gith…
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The DiffUSE Project retweeted
We are SO lucky to have @stephanie_mul joining Radial to lead @diffUSEproject 🙌🏼
I'm ecstatic to share that I'm joining @diffUSEproject full-time as Scientific Program Director at @AsteraInstitute.
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Congrats to DiffUSE lead Stephanie Wankowicz, @stephanie_mul, on winning the inaugural Sheldrick Award! Her work on entropic flexibility and reproducibility in structural biology is core to what we're building. aucryst.org/sheldrick-award/…
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The DiffUSE Project retweeted
Mar 13
Another day, another open-source useful tool coming out of @diffUSEproject . Announcing Sampleworks - a framework for integrating structural biology observables, structure predictors, and guidance to improve the modeling of conformational ensembles.
Excited to share Sampleworks, part of the @diffUSEproject. It's a modular framework connecting structure predictors (Boltz-1/2, Protenix, RF3) to experimental data and guidance methods. Swap predictors or guidance methods. diffuse.science/posts/sample…
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The DiffUSE Project retweeted
Mar 12
The diffUSE project is expanding, both in people and in scope! We are incredibly lucky to have @stephanie_mul coming on board full-time to lead science across the project. Check out the awesome explainer video, and Stephanie's blog post going into more detail below 👇
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The DiffUSE Project retweeted
Stay tuned for more soon, and check out the code here - github.com/diff-use/samplewo…. We hope others will build off/contribute to this. Also, we are expanding this team - see job posting here diffuse.science/work-with-us….
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The DiffUSE Project retweeted
We observed a tradeoff: weak guidance improves fit to data without wrecking protein geometry. But strong guidance destroys the geometry. Interestingly, models differ a lot in how they handle this despite similar architectures.
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The DiffUSE Project retweeted
Excited to share Sampleworks, part of the @diffUSEproject. It's a modular framework connecting structure predictors (Boltz-1/2, Protenix, RF3) to experimental data and guidance methods. Swap predictors or guidance methods. diffuse.science/posts/sample…
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The DiffUSE Project retweeted
Mar 11
We're expanding our life sciences work through a new division Radial led by @beckypferdehirt as CEO. Becky be work closely w @PracheeAC @seemaychou to help lead experiments with infrastructure and approaches to funding, enabling, and publishing science 1/
A new nonprofit called Radial is launching with at least $500 million to modernize the scientific process for the AI era. trib.al/yfGSUvt
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